JAL-3633 Help documentation updated

[jalview.git] / README

diff --git a/README b/README
index eaf226b..e8c44a9 100755 (executable)
--- a/README
+++ b/README
@@ -16,18 +16,48 @@ You may also be able to use Borland JBuilder to build Jalview. A JBuilder projec
 but the library dependencies are almost certainly out of date. See the build.xml 
 for current dependencies.
 
+##
+
+Jalview-JS
+
+To enable transpilation of Jalview's code:
+
+1. Locate the 'dropins' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it.
+  - typically it is at the top of the Eclipse installation, or on OSX under Eclipse.app/Contents/Eclipse
+  
+2. Restart Eclipse
+
+3. If all is well you should see the 'Java2Script' builder is listed as the primary builder for the Jalview project.
+  if not, this is because your properties file needs to have the standard java builder replaced with the following:
+  <name>net.sf.j2s.core.java2scriptbuilder</name>
+
+- otherwise Javascript files will now be generated in the site/swingjs/j2s directory whenever a build occurs
+
+4. Execute the 'unzip-to-site' task (if it isn't automatically run) to update the site directory with the latest versions of SwingJS, varna-js, JSmol and other dependencies required by Jalview.
+
+
+  
+
+
+##
+
 For more help, read the file doc/building.html
 
 
 ##################
 
-To run application:
+To run application...
+[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
+  ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]
 
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+on Windows use:
+  java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+and on MacOS or Linux:
+  java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
 
 Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
 
-java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+  java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
 
 
 ##################